Inputs and Modes

After generating your systematic noise file, you can run the DRAGEN for IDT Custom Panels variant calling pipeline. The pipeline is pre-optimized for IDT xGen cfDNA and FFPE library chemistry, so you do not need to adjust calling parameters manually.

Required Inputs

• Sample reads: FASTQ, BAM, CRAM, or ORA files

• Systematic noise file (from Stage 1)

• Target panel BED file

• (Optional) Block-zone BED file for additional filtering

Choose Your Launch Path

• Option A: Launch from Run Planner — for new sequencing runs (tumor-only).

• Option B: Launch from BSSH or ICA — for existing data or tumor-normal analysis.

Sample Type Considerations

If you are working with formalin-fixed paraffin-embedded (FFPE) samples that show significant DNA degradation, see Low-Quality FFPE Mode before launching.